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In 1988, Richard Lenski's lab began an experiment. A set of 12 bacterial cultures were started, but only given enough sugar to keep them growing for a few hours. The next day, the bacteria were again given another burst of sugar. And the process has been repeated every day since. The goal? To be able to follow major evolutionary innovations as bacteria try to outcompete their peers under near-starvation.

Back in 2008, one of the 12 cultures had its big breakthrough, a sudden burst of growth powered by citrate, a chemical that was present in the mix, but not normally used by bacteria (a result that was hilariously contested by the founders of Conservapedia). Now, Lenski is benefitting from a technology that didn't exist when he started the work—whole genome sequencing—and reconstructing exactly how the bacteria evolved the new ability.

The team behind the latest work took advantage of the fact that the experiment has involved taking snapshots of the bacteria every few thousand generations, simply by siphoning a few off and sticking them in the freezer. These bacteria can be used to figure out what the status of the genomes were at a given generation, or even grown again, to see whether the same evolutionary history can take place.

In the new paper, the authors sequence the genomes of 29 different clones of bacteria, obtained from various points in the culture's history. One distinct genetic lineage appeared in the culture a bit before 10,000 generations but had apparently died off before 20,000 generations, never to be seen again (the authors called this UC, for "unsuccessful clade"). Three large groups of related strains still persist in the cultures, but only one of them has citrate-eating bacteria, which evolved sometime around 31,000 generations in.

The first citrate-eating bacteria appear to have left a lot of descendants, since that group has diversified rapidly (although it hasn't completely killed off its competition). In fact, one branch of the citrate eaters has picked up a mutation that wipes out a gene involved in DNA repair, which causes an increased rate of mutation and an even faster diversification.

The genomes also let the researchers figure out exactly how citrate eating evolved. The E. coli used in the experiment actually have a gene that brings citrate inside the cell, but it's normally shut down when oxygen is present. In the first citrate eaters, a bad duplication of this gene made an extra copy, but put it under the control of regulatory DNA for a neighboring gene. This worked, in that the new control sequence expressed the gene even when oxygen was around, but it didn't work well. The resulting bacteria only had a one percent advantage in reproductive success relative to their peers.

Things accelerated afterwards, as further duplications put more and more copies of the newly generated gene into the genomes. By the time there were three copies of this gene present, the bacteria had a large competitive advantage. Presumably, somewhere in Michigan, their descendants are fine-tuning that ability even as you read this.

On its own, this would be a great story, as the researchers have traced the evolution of a complex trait that's so rare that it took tens of thousands of generations of bacteria to produce it. But the authors also show there's still a bit of mystery to their system. They had previously showed that some specific change had occurred somewhere near 20,000 generations that made evolving citrate-eating more probable.

So, the authors took a copy of the newly evolved citrate transporter gene, and inserted it into bacteria from earlier in the history. Although it worked, in that they could eat citrate, it worked very poorly. The same problem occurred when the gene was placed in lineages that had split off prior to 20,000 generations. So, what happened at 20,000 generations that makes citrate easier to deal with?

They don't know. Sequencing the genomes reveal a variety of changes, but none of them would obviously make digesting citrate easier. So, even as this experiment goes on, it's got some of the researchers scratching their heads about its past.

Thank you John for this most informative, accessible and entertaining article. As with others who have commented above, this is exactly why Ars is one of my absolute favorite daily stops. Other places may cover more science news, but almost none take the time to write with such great perspective. It's rare and precious, and extremely relevant to a computer geek who needs (philosophically) to not be clueless about science, but wouldn't know where to begin following what's important in biology or many other fields. You do a great service, and I would sorely miss it were it gone.

Very important research, with interesting results. Who paid for this research? If we did (U.S. Government) why is the report behind a $35 paywall???

Because the US government did not pay for publication, distribution, editors, or management of the peer review process. That is what the paywall (and subscription fees etc) is trying to recoup.

This model has been gradually shifting as things move to digital but that's a slow process. We're not at the point where there are no printing costs yet. Even once we reach that, there are costs of making files available on line, in addition to the editing, peer review, etc.

To put it another way, the US government pays for the federal highway system, right? But there are still tolls. The US government pays for the Navy but they won't let us fly an F16. The US government has purchased tons of oil, stored in the strategic petroleum reserve, but they won't give us any. Your taxes are not sufficient to make everything free.

Regrettably the presence of overwhelming empirical evidence means nothing to some cultural conservatives who are willing to attack science itself (inconvenient as it can be to dogmatic views).

Sadly, millions of American kids are being taught at home and in church to distrust scientists. I just hope some of them learn critical thinking and reasoning in spite of this.

Regrettably, this overwhelming empirical evidence is used to mislead people into believing evolution ever happened. It turns out that this empirical evidence is all about MICRO evolution, but the word MICRO was, for some reason, omitted. The article does sound like powerful proof, but it is only deceit at its best (if it's intended to promote the theory).

Try and see if these researchers can provide you with an explanation for the appearance of the highly complex codes inside cells.

BTW, I've always wondered what programmers think about the codes inside cells. I mean, do programmers who have a clue about the complexity of the codes inside cells (much more complex than the ones they ever wrote) believe they came into existence on their own?

Regrettably the presence of overwhelming empirical evidence means nothing to some cultural conservatives who are willing to attack science itself (inconvenient as it can be to dogmatic views).

Sadly, millions of American kids are being taught at home and in church to distrust scientists. I just hope some of them learn critical thinking and reasoning in spite of this.

Regrettably, this overwhelming empirical evidence is used to mislead people into believing evolution ever happened. It turns out that this empirical evidence is all about MICRO evolution, but the word MICRO was, for some reason, omitted. The article does sound like powerful proof, but it is only deceit at its best (if it's intended to promote the theory).

Try and see if these researchers can provide you with an explanation for the appearance of the highly complex codes inside cells.

BTW, I've always wondered what programmers think about the codes inside cells. I mean, do programmers who have a clue about the complexity of the codes inside cells (much more complex than the ones they ever wrote) believe they came into existence on their own?

We have a contestant!Edit: BTW, you seem to imply that "complexity" is a sign of sophistication. It's not. Horrible spaghetti code is complex, doesn't mean it's good code.

It's amazing that these scientists chose willingly not to include the phrase "micro" into their work. Just because there is no such thing, they should totally be willing to pretend that my fantasy land explanation for how we actually have evidence of evolution is real. My taxes pay their salary, their research should therefore accept my non-scientific nomenclature.

Also, "code" when used in cells is literally the same thing as "code" used in computers. FYI.

Regrettably the presence of overwhelming empirical evidence means nothing to some cultural conservatives who are willing to attack science itself (inconvenient as it can be to dogmatic views).

Sadly, millions of American kids are being taught at home and in church to distrust scientists. I just hope some of them learn critical thinking and reasoning in spite of this.

Regrettably, this overwhelming empirical evidence is used to mislead people into believing evolution ever happened. It turns out that this empirical evidence is all about MICRO evolution, but the word MICRO was, for some reason, omitted. The article does sound like powerful proof, but it is only deceit at its best (if it's intended to promote the theory).

Try and see if these researchers can provide you with an explanation for the appearance of the highly complex codes inside cells.

BTW, I've always wondered what programmers think about the codes inside cells. I mean, do programmers who have a clue about the complexity of the codes inside cells (much more complex than the ones they ever wrote) believe they came into existence on their own?

BTW, I've always wondered what programmers think about the codes inside cells. I mean, do programmers who have a clue about the complexity of the codes inside cells (much more complex than the ones they ever wrote) believe they came into existence on their own?

Regrettably the presence of overwhelming empirical evidence means nothing to some cultural conservatives who are willing to attack science itself (inconvenient as it can be to dogmatic views).

Sadly, millions of American kids are being taught at home and in church to distrust scientists. I just hope some of them learn critical thinking and reasoning in spite of this.

Regrettably, this overwhelming empirical evidence is used to mislead people into believing evolution ever happened. It turns out that this empirical evidence is all about MICRO evolution, but the word MICRO was, for some reason, omitted. The article does sound like powerful proof, but it is only deceit at its best (if it's intended to promote the theory).

Try and see if these researchers can provide you with an explanation for the appearance of the highly complex codes inside cells.

BTW, I've always wondered what programmers think about the codes inside cells. I mean, do programmers who have a clue about the complexity of the codes inside cells (much more complex than the ones they ever wrote) believe they came into existence on their own?

You tell'em Clem! And while you're at it, send me a link to that homosexual de-programming clinic again wiil you? The first time didn't take!

Regrettably the presence of overwhelming empirical evidence means nothing to some cultural conservatives who are willing to attack science itself (inconvenient as it can be to dogmatic views).

Sadly, millions of American kids are being taught at home and in church to distrust scientists. I just hope some of them learn critical thinking and reasoning in spite of this.

Regrettably, this overwhelming empirical evidence is used to mislead people into believing evolution ever happened. It turns out that this empirical evidence is all about MICRO evolution, but the word MICRO was, for some reason, omitted. The article does sound like powerful proof, but it is only deceit at its best (if it's intended to promote the theory).

Try and see if these researchers can provide you with an explanation for the appearance of the highly complex codes inside cells.

BTW, I've always wondered what programmers think about the codes inside cells. I mean, do programmers who have a clue about the complexity of the codes inside cells (much more complex than the ones they ever wrote) believe they came into existence on their own?

You tell'em Clem! And while you're at it, send me a link to that homosexual de-programming clinic again wiil you? The first time didn't take!

I sympathize. Codes don't come into existence on their own. You know that, but won't admit it. Since you can't answer you dodge the issue.

BTW, I've always wondered what programmers think about the codes inside cells. I mean, do programmers who have a clue about the complexity of the codes inside cells (much more complex than the ones they ever wrote) believe they came into existence on their own?

I have bachelor's degrees in both math (studying computer science) and biology (studying molecular biology). So I do in fact "have a clue about the complexity of the codes inside cells".

And my first observation is that I have written code much, much more complex than that inside many cells. Most bacteria genomes are only a few kB in length, and I've written both applications (e.g. VMware Workstation 4 UI, written almost entirely by me and over 100K lines of code) and libraries which were more than 10x larger.

My second observation is that the code inside cells looks like it was written by a group of exceptionally retarded monkeys hitting keys at random. Granted, this isn't *that* much worse than some of the computer code I've seen over the years (which after all was written by slightly less retarded monkeys hitting the keys almost at random). More specifically, code inside cells consists largely of large regions badly copy/pasted, with spelling errors and appalling amounts of barely functioning garbage.

My final observation is that you, having almost zero knowledge of CS and mol bio, seem strangely convinced that people who do have such knowledge would support your idiotic position.

In conclusion, you are an enourmous tool, and should probably never post in the interwebs again.

The fundies are here now. "Look, look, they didn't use the word 'micro' -- this study is misleading and deceitful, waaaah." -- Just like shady lawyers and crooked politicians, they're trying to start an argument about something bogus and silly, and get everyone's attention off the fact that THEY'VE BEEN PROVEN WRONG.

Hey fundies, explain this if you would: Your thousands-year-old book says this can't happen, because these e. coli bacteria were created "perfect." So how can you explain this result? I'd ask you to quote Scripture, but I'm sure you know only the verses your cult leader taught you.

I sympathize. Codes don't come into existence on their own. You know that, but won't admit it. Since you can't answer you dodge the issue.

If I drop a bucket full of 1's and 0s onto the floor randomly, it actually is a generation of code. Inefficient code, possibly meaningless. Of course, chemistry doesn't work like code, insofar as there are actually certain elements that inherently are drawn to each other and react in a given way. Nevertheless, even assuming no preset desirable machinations, if I then continue to add 1s and 0s, removing junk code as I go, I will eventually get a series of workable code. Continue adding 1s and 0s and you will get more complex code. If your code starts performing a specific function (it becomes an RSS reader, say), you can remove code that does not help it perform this role. Thus, your code will become a specific type of program.

Do this again, and you'll get a different program.

The point is that over billions of years, the amount of random generation, removal of junk, and continual adding of resources will continuously generate more complex code, Sorta like over billions of years, creatures could become more complex.

Regrettably the presence of overwhelming empirical evidence means nothing to some cultural conservatives who are willing to attack science itself (inconvenient as it can be to dogmatic views).

Sadly, millions of American kids are being taught at home and in church to distrust scientists. I just hope some of them learn critical thinking and reasoning in spite of this.

Regrettably, this overwhelming empirical evidence is used to mislead people into believing evolution ever happened. It turns out that this empirical evidence is all about MICRO evolution, but the word MICRO was, for some reason, omitted. The article does sound like powerful proof, but it is only deceit at its best (if it's intended to promote the theory).

Try and see if these researchers can provide you with an explanation for the appearance of the highly complex codes inside cells.

BTW, I've always wondered what programmers think about the codes inside cells. I mean, do programmers who have a clue about the complexity of the codes inside cells (much more complex than the ones they ever wrote) believe they came into existence on their own?

You tell'em Clem! And while you're at it, send me a link to that homosexual de-programming clinic again wiil you? The first time didn't take!

I sympathize. Codes don't come into existence on their own. You know that, but won't admit it. Since you can't answer you dodge the issue.

You don't actually know that.

Let us accept your premise for a moment (even though it's wrong. DNA is nothing like machine code).We have two instances of programming: that created by humans, and that shown in cell nuclei.Your logic is that because one is designed, the other must be designed too. Because "complexity".

Never mind evidence actually showing how such things gain in complexity over time (this article actually demonstrates a genome getting more complex), because if something is complex that means someone made it. There are often arguments made by climate skeptics based upon the premise that the climate is actually too complex to understand. Yet we've got a fairly good idea of how such a thing arose in nature. The only way to say that complexity == design would be to base it off the premise that every instance of complexity that we've seen so far in nature has been designed in the first place, which isn't the case.

Regrettably the presence of overwhelming empirical evidence means nothing to some cultural conservatives who are willing to attack science itself (inconvenient as it can be to dogmatic views).

Sadly, millions of American kids are being taught at home and in church to distrust scientists. I just hope some of them learn critical thinking and reasoning in spite of this.

Regrettably, this overwhelming empirical evidence is used to mislead people into believing evolution ever happened. It turns out that this empirical evidence is all about MICRO evolution, but the word MICRO was, for some reason, omitted. The article does sound like powerful proof, but it is only deceit at its best (if it's intended to promote the theory).

Try and see if these researchers can provide you with an explanation for the appearance of the highly complex codes inside cells.

BTW, I've always wondered what programmers think about the codes inside cells. I mean, do programmers who have a clue about the complexity of the codes inside cells (much more complex than the ones they ever wrote) believe they came into existence on their own?

Not sure if serious."New Poster" flag is damning.

Its unfortunate that people like this do not have a clue on what they are talking about. I doubt he has ever taken a statistics class, or a biology class, or programming class and is not suited to talk about any of the aforementioned topics.

What would be really exciting is if they were to find that some of the frozen samples had managed to reproduce and mutate in an extremely low metabolic state. Of course it would royally screw up any quantitative results they've compiled.